Mining genomic data to understand diseases

Summary

In this project, we aim to develop, apply ,and enhance bioinformatics and statistical tools to effectively collate, query, and mine public data repositories of transcription factor binding data in systematic ways.

Supervisor(s)

Dr Matloob Khushi

Research Location

Westmead - Childrens Medical Research Institute

Program Type

Masters/PHD

Synopsis

Many cellular functions are mediated by sequence-specific DNA-binding proteins, called transcription factors that regulate gene expression. Transcription factor binding to DNA, either alone or as part of a complex with other proteins, is influenced by epigenetic modifications and small sequence variations or SNPs (Single Nucleotide Polymorphisms).  Perturbation of transcription factor binding plays a role in many diseases, including but not limited to cancer. Therefore, the characterisation of transcription factor binding sites across the genome using next-generation technologies (e.g. ChIP-seq) has been a focus of research in recent years. Much of these data are now available in public repositories but under-utilised. Cell-specific gene expression and structural variant datasets are also available.

In this project, we aim to develop, apply and enhance bioinformatics and statistical tools to effectively collate, query, and mine public data repositories of transcription factor binding data in systematic ways. These tools will then enable us to perform integrated and intelligent e.g. machine learning analyses on the collected data to identify novel, biologically relevant discoveries.

Students will get experience in computational biology, computer programming, and bioinformatics related to current biological problems.

Additional Information

Children's Medical Research Institute (CMRI) is an award-winning state-of-the-art medical research facility, with over 100 full-time scientists dedicated to researching the genes and proteins important for health and human development. The CMRI is supported in part by its key fundraiser Jeans for Genes®. Our scientists are internationally recognised research leaders and foster excellence in postgraduate training. CMRI graduates are highly sought after nationally and internationally.

CMRI is located at Westmead, a major hub for research and medicine in NSW, and is affiliated with the University of Sydney. Easy to access by public transport.

We are looking for top quality students who can prove a dedicated interest and enthusiasm for scientific research.

Candidates may apply for a CMRI PhD Research Award, which exceeds the Australian Postgraduate Awards and NHMRC scholarships in value. Visit the CMRI website for more details

Eligibility:
PhD entry: Honours Class I
Understanding of cell biology and knowledge of any computer language e.g. python, C/C++, Perl, or Java

Want to find out more?

Contact us to find out what’s involved in applying for a PhD. Domestic students and International students

Contact Research Expert to find out more about participating in this opportunity.

Browse for other opportunities within the Westmead - Childrens Medical Research Institute .

Keywords

Bioinformatics, Cancer, Machine learning, transcription factor

Opportunity ID

The opportunity ID for this research opportunity is: 2076

Other opportunities with Dr Matloob Khushi